Antiretroviral therapy (ART) reduces mortality and morbidity in HIV-infected individuals. With successful therapy HIV RNA becomes undetectable, but drug resistance may occur. Specific HIV mutations are associated with resistance and these mutations can be detected through standard genotypic resistance tests, which have the ability to detect mutations only when they are present in approximately 20% of the virus population within an individual. Importantly, it is now known that the presence of certain resistance mutations, even at very low concentrations within a patient?s virus population (1% or more), can contribute to virological failure. These drug resistant minor variants can reflect the early emergence of acquired resistance during therapy, and can also be transmitted to newly infected individuals. These minor variants are not detected by standard drug resistance assays and methods to detect minor variants that contribute to HIV virological failure are needed. These assays would need to detect mutations causing resistance to each of the antiretroviral drug classes (NRTI, NNRTI, PI and INI) in all HIV subtypes, and must be inexpensive, since large numbers of patients would need to be screened. The goal of this project is to develop an assay to detect minor populations of resistant variants in blood specimens from HIV-infected individuals with HIV RNA viral loads above 1000 copies/ml.